Tips on Writing Your Thesis

Senior Exercise Performance Contract

Good writing in scientific disciplines
is not significantly different from good writing in other disciplines. The rules of good grammar, punctuation, and
style all apply. Precision and clarity
of expression and good organization are essential. To be sure, one must master a vocabulary,
quite large in some fields. This
vocabulary can be intimidating, perhaps because scientific terminology is
usually very precise in meaning, and because it is often based in Latin and
Greek roots. However, excessive use of
jargon can make a scientific paper nearly unintelligible. In addition, there are some conventions
unique to scientific writing. Some of
these conventions are listed below, but others are not easy to describe. A paper written outside these conventions may
be technically correct but just does not "feel" right. The best advice is to take note of good
writing as you read scientific papers.
But note also that not all published papers are well written!

Write to illuminate, not to
confuse. Use the simplest language
consistent with that goal. Write clearly
and concisely, using correct grammar and spelling. Organize and express your thoughts clearly
and succinctly. Eliminate irrelevant
information, no matter how interesting it is, and no matter how hard you worked
to ferret it out.

Have someone (in addition to your
faculty readers) read your drafts before you produce the final copy. Have them tell you whether the organization
and style make sense; ask all of your reviewers to be frank and honest. Some people read their papers out loud
rapidly; if you stumble while doing this, you probably need to make significant
improvements. Poorly written reports will
receive lower grades.

Your thesis must be double-spaced on
8-1/2" x 11" paper, with a left-hand margin of at least one
inch. Be sure that the printout is
legible and that all required features of scientific writing, such as italicizing
scientific names (Nereis succinea),
formulae with subscripts (H2CO3), and units with
superscripts (K+, cm-2, m2, etc.) are correct. If you use Greek letters, be sure they print
correctly (m and
b, not m and b).

Some other important conventions in
scientific writing are:

It is perfectly acceptable, even preferable,
that you write in the first person. In
fact, doing so often makes your writing much clearer and stronger, e.g. "I
chose this experimental system because..." or "I hypothesize
that...."

Spell out completely all words and phrases
you intend to abbreviate the first time you use the term; use a minimum of
abbreviations, or your thesis will resemble an alphabet soup. Excessive use of abbreviations and acronyms
can destroy comprehensibility.

Use present
tense for facts and other commonly accepted knowledge; e.g., “ATP is the energy currency of the cell.” Use past
tense for historical events, and for what other people did; e.g., "Wong (1983) showed
that Species Y is a protandrous hermaphrodite that breeds from May through
August. Wong (1983) also noted that
Species Y did not breed in 1980, because the environment never reached the
critical temperature."

Avoid jargon and freight train
constructions. A freight train is a
sequence of nouns masquerading as adjectives.

Use the correct singular and plural forms of
all words. Be aware that datum, phenomenon, criterion, medium
are pluralized as data, phenomena,
criteria, and media,
respectively. Always make your subject
and verb agree in number.

Number your pages on ALL drafts.

Always italicize
scientific names of organisms. Do not
italicize the names of higher taxa, such as families, classes, or phyla, or of
common names.

Scientific names are always taken as singular, no matter how many individuals
are indicated: "Thiara granifera
was collected from Whitefield Creek." vs. "Snails were collected from
Whitefield Creek."

When you finish writing your thesis,
proofread it very carefully. Ask
yourself again if each sentence you wrote is the most meaningful, concise,
and truthful statement that you can possibly make. After printing it out, proofread it again and
ask a friend to do so as well.

Some General Advice

Your Audience

Before
writing any document you need a clear idea about your audience. For a senior thesis, write for an audience of
senior biology majors, i.e. readers who have a broad background in biology in
general, who are familiar with basic scientific ideas, but who are not experts
in the specific area you have chosen for study.
Keeping this audience in mind should make it easier to decide how much
information to include and what to leave out.

Give Yourself Time

No writer (except
Isaac Assimov, perhaps) can produce a clear, well-organized document in one
sitting. An essential part of the
writing process is getting the creative juices flowing, a process that goes on
more or less subconsciously once you have generated a few fundamental
ideas. Sit down early and sketch out a
few ideas or an outline, then push this paper aside for a week or so. The ideas will perk in your brain, the things
you want to say will start to take shape -- a few opening sentences may even
occur to you in the shower. Take
advantage of this subconscious process; it will save you much painful time
later and will allow you to avoid those all-nighters where you sit in front of
a blank computer screen trying to force words that won't come. Giving yourself plenty of time will also make
it possible for you to get feedback on your drafts from others; all good writers
gather advice from their colleagues about their writing.

Look
at Some Models

If you are unclear
about what your finished document should look like, look at some successful
models: theses written by students who have already graduated. These are on file in the Biology Department
office and can be checked out for short period of time (a few days) from the
Biology department administrator. But
don't read random theses; you need to look at the best ones if you are
going to use them as models. So ask your
faculty advisors for names of students who wrote particularly good theses. Choose theses to read that are the same type
(proposal or experimental) as yours, and it is best to find some to read that
address the same type of biology you are examining.

Text Citations in Scientific Writing

It is absolutely necessary to indicate
with text citations the sources of

all
material that you discuss that is not original (your own), including both facts
and ideas (see Honesty in Writing,
below). There are two parts to proper
citations: the text citations
themselves, and the Literature Cited
section at the end of the thesis. Note
that scientific style in this respect is very different from the style used in
the humanities. For example, avoid the
use of ibid. or loc. cit., and superscripts5 and numbers (2) completely. Do not use direct quotes from the literature;
instead of quoting directly, rephrase in your own words and credit the source
appropriately.

Text
citations. There must be a text
citation for each non-original item in your thesis, including facts and ideas
as well as apt phraseology. When you
state a fact or idea beyond common knowledge, you must give a reference to that statement in the form of a text
citation. Citations in the text should
be in the form of: "Faha (1998) stated that black is black." or
"Black was demonstrated to be white (Loving and Sundberg,
2003)." Always cite all authors of
multiple-authored papers, as "Chang and Lee (1995) observed...." If
there are three or more authors, cite their paper as in the following: "Marsh snails were found in blah blah
blahty-blah (Sbertole et al.,
(2004)." [et al. is the contraction of the Latin et alii, which means "and others."] If an entire paragraph discusses information
from one source, you can probably write the passage so that it is clear that
the entire paragraph has non-original material from that single source. If a paragraph includes material from several
sources (the more usual case), then you will have to use a text citation for
each of the sources. Parenthetical text
citations go inside terminal punctuation, as (Minehart, 2006).

Literature
Cited. Please note that this section
is called Literature Cited, and not Bibliography or References. List papers alphabetically by first author,
and then by date if you cite more than one paper with the same first
author. The format of these citations is
standard and can be found in articles published in any of the major research
journals, though usually each journal will have a few idiosyncrasies. The best
practice is to follow the citation format found in one of the major journals in
the field of biology in which you are working.
Beware, however, of some journals, such as Science and Nature,
use a shortened format that is not very informative: avoid these styles. In all
your citations, be sure to include the title of the journal article and
inclusive pagination. The usual sequence
is: author(s), year, article title, journal name, volume, inclusive pages. Pay close attention to proper use of
punctuation and abbreviations in reference lists. Here is an example of one correct style for a
typical journal article:

It is always awkward to deal with secondary sources, that is, the
situation where you are referring to work published by Person A, but getting
your information about that work not from a paper authored by A, but from a
paper published by Person B. It is
improper to cite Paper A, as you did not read it yourself. But you may want to acknowledge the work of
Person A, even though you read only Paper B.
Further complicating matters, Person B might have misinterpreted or
misquoted Paper A. If you choose to cite
the work of Person A under these circumstances, your Literature Cited section
must list only Paper B. In the text you
might write, "According to Franszicek (1980), Darwin in 1859 concluded . .
. ." An alternative approach is: "Fact fact fact (Darwin, 1859, as
cited by Franszicek, 1980)." Of
course, the very best approach is to actually read the paper by Person A.

Citing sources on the Web:

in word,
DON’T. Possible exceptions might be a
photograph you wish to use to illustrate something or a maybe a figure or
drawing that represents someone else’s model that is not found anywhere in a
primary reference. If you wish to use a
web citation, be sure to clear it with your advisor(s) well in advance of
turning in a draft.

Honesty in Writing

We expect the ideas in all your writing
for your thesis to be the original products of your own reflections and
analyses. Of course, you will not derive
these ideas in a vacuum; they will arise from a combination of your study of
the ideas of others and your own original contributions. It is therefore necessary for you to make a
careful distinction between ideas that you adopt from other sources, and those
you develop yourself.

You do this by citing in the text the
sources of those ideas from others that you adopt or discuss in your
thesis. We must assume that any ideas
that you do not cite as coming from others are your own. If that is not the case, then you are being
dishonest about the intellectual origins of your thesis. When in doubt, cite. Anything
you say that is not general knowledge should be supported by a reference. Whether you learn something from reading,
from a class lecture, or from discussions with others, you must acknowledge the
source when you use that information in your thesis. This applies not only to factual information
but also to ideas. Failure to
acknowledge your sources will be treated as a violation of the rules for
academic honesty.

It may appear to you that these rules
are somewhat harsh, but in fact they are fundamental to the practice of
science. Science is a collection of
ideas about the way that nature "works", ideas refined by experiment
and observation. People who contribute
these ideas are entitled to the credit for them. It is no more proper to borrow an idea without
giving credit to the source than it is to borrow a car without asking the
owner's permission. You will want to be
recognized and acknowledged for your own original contributions; it is only
fair that you accord the same treatment to others.